Abstract
The Vaginal Microbiome: Disease, Genetics and the Environment
Highlights
This manuscript is part of a pilot effort on the part of NIH staff and the Nature publishing group to provide a more convenient archive for "marker papers" to be published
Gross alterations in the vaginal microbiome are frequently observed in women with bacterial vaginosis, but the exact etiology of this disorder is still unknown
We have proposed to address the following questions: 1. Do the genes of the host contribute to the composition of the vaginal microbiome? We hypothesize that genes of both host and bacteria have important impacts on the vaginal microbiome
Summary
The 16S rDNA post-sequencing analysis pipeline is designed to filter the reads based on quality, to trim the barcode (Multiplex Identifier) and PCR amplification primer sequences, and to assign taxonomy to the high quality reads obtained. 80% of the reads are retained after the application of these quality control metrics These high quality reads are assigned taxonomy using the RDP Classifier (1) with a minimum bootstrap confidence of 80%. Sequences are assembled using Velvet (2), Newbler (Roche Diagnostics) or other appropriate assembler Sequences of these bacterial clones will meet or exceed ‘Standard Draft’ quality as defined in Chain et al (3). We have compared the complete genome sequences from a panel of Gardnerella vaginalis (4), Lactobacillus sp., Sneathia, and other isolates (in preparation), taken from our samples
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